Method and systems for characterizing skin related conditions

Patent metadata

Field	Value
Publication number	US-10169541-B2
Application number	US-201715497072-A
Country	US
Kind code	B2
Filing date	Apr 25, 2017
Priority date	Oct 21, 2014
Publication date	Jan 1, 2019
Grant date	Jan 1, 2019

Abstract

Embodiments of a method and system for characterizing a skin-related condition in relation to a user can include one or more of: a handling network operable to collect containers comprising material from a set of users, the handling network comprising a sequencing system operable to determine microorganism sequences from sequencing the material; a microbiome characterization system operable to: determine at least one of microbiome composition data and microbiome functional diversity data based on the microorganism sequences, collect supplementary data associated with the skin-related condition for the set of users, and transform the supplementary data and the at least one of the microbiome composition data and the microbiome functional diversity data into a characterization model; and a therapy system operable to promote a treatment to the user for the skin-related condition based on characterizing the user with the characterization model in relation to the skin-related condition.

First claim

We claim:

1. A system for evaluating a skin-related condition in relation to a user, the system comprising:
a handling network operable to collect containers comprising material from a set of users, the handling network comprising:
a library preparation system operable to fragment and perform multiplex amplification on the material using a primer compatible with a genetic target associated with the skin-related condition;
a sequencing system operable to determine microorganism sequences from sequencing the material;

a microbiome characterization system operable to:
determine microbiome composition data and microbiome functional diversity data based on an alignment between the microorganism sequences and reference sequences associated with the skin-related condition,
collect supplementary data associated with the skin-related condition for the set of users, and
transform the supplementary data and features extracted from the microbiome composition data and the microbiome functional diversity data into a characterization model for the skin-related condition; and

a treatment system operable to provide a treatment to the user for the skin-related condition based on characterizing the user with the characterization model in relation to the skin-related condition.

2. The system of claim 1 , wherein the microbiome characterization system is further operable to:
obtain a set of skin-related feature-selection rules correlating the skin-related condition to a subset of microbiome composition features and a subset of microbiome functional diversity features; and
generate the features based on evaluating the microbiome composition data and the microbiome functional diversity data against the set of skin-related feature-selection rules, wherein the set of skin-related feature-selection rules are operable to improve the microbiome characterization system by facilitating decreased processing time to transform the supplementary data and the features into the characterization model.

3. The system of claim 2 , wherein the microbiome functional diversity features comprises at least one of: a cluster of orthologous group of proteins feature, a genomic functional feature, a taxonomic feature, a chemical functional feature, and a systemic functional feature.

4. The system of claim 1 , wherein the handling network further comprises a library preparation system operable to fragment and perform multiplex amplification on the material using a primer compatible with a genetic target associated with the skin-related condition.

5. The system of claim 1 , further comprising an interface operable to improve display of skin-related condition information derived from the characterization model, wherein the skin-related condition information comprises a microbiome composition for the user relative to a user group sharing a demographic characteristic, and wherein the microbiome composition comprises a set of taxa comprising at least one of: Marvinbryantia (genus), Erysipelotrichales (order), Erysipelotrichia (class), Bacteroidetes (phylum), Staphylococcus (genus), Staphylococcaceae (family), Bacillales (order), Actinobacteria (class), Firmicutes (phylum), Actinobacteria (phylum), and Propionibacterium (genus).

6. The system of claim 5 , wherein the skin-related condition information comprises a change in the microbiome composition over time and a change in a microbiome functional diversity over time in relation to the treatment and the skin-related condition.

7. The system of claim 1 , wherein the features comprise at least one of a Kyoto Encyclopedia of Genes and Genomes (KEGG) functional feature and a Clusters of Orthologous Groups (COG) functional feature, and wherein the features comprise transformation microbiome features derived from at least one of: a relative abundance monotonic transformation and a non-monotonic transformation.

8. The system of claim 7 , wherein the transformation microbiome features are associated with at least one of: a normalization, a feature vector derived at least one of linear latent variable analysis and non-linear latent variable analysis, linear regression, non-linear regression, a kernel method, a feature embedding method, machine learning, and a statistical inference method.

9. The system of claim 7 , wherein the skin-related condition comprises dry skin, and wherein the features comprise a microbiome composition feature associated with a relative abundance of at least one of: Staphylococcus (genus), Staphylococcaceae (family), Bacillales (order), Actinobacteria (class), Firmicutes (phylum), Actinobacteria (phylum), and Propionibacterium (genus).

10. A method for characterizing a skin-related condition in relation to a first user, the method comprising:
generating a microbiome composition dataset and a microbiome functional diversity dataset based on microorganism sequences derived from biological samples from a set of users, wherein generating the microbiome composition dataset and the microbiome functional diversity dataset comprises:
identifying primers for nucleic acid sequences associated with the skin-related condition,
fragmenting nucleic acid material,
amplifying the fragmented nucleic acid material using the identified primers, and
determining an alignment of the microorganism sequences to reference sequences associated with the skin-related condition;
receiving a supplementary dataset informative of the skin-related condition for the set of users;
obtaining a set of skin-related feature-selection rules correlating the skin-related condition to a subset of microbiome composition features and a subset of microbiome functional diversity features;
generating a feature set based on evaluating the microbiome composition dataset and the microbiome functional diversity dataset against the set of skin-related feature-selection rules;
applying the feature set with the supplementary dataset to generate a characterization model for the skin-related condition;
generating a first characterization of the first user in relation to the skin-related condition using the characterization model; and
providing a therapy to the first user for the skin-related condition based on the first characterization.

11. The method of claim 10 , wherein the characterization model is an eczema-related characterization model, the method further comprising:
generating a second feature set based on the microbiome composition dataset and the microbiome functional diversity dataset;
applying the second feature set to generate a scalp-related characterization model; and
generating a second characterization of the first user in relation to a scalp-related condition using the scalp-related characterization model.

12. The method of claim 11 , further comprising:
generating a third characterization of the first user in relation to a dry skin-related condition using a dry skin-related characterization model;
wherein promoting the therapy to the first user comprises promoting the therapy based on the first, second, and third characterizations.

13. The method of claim 10 , wherein promoting the therapy comprises automatically initiating a signal that controls a treatment system to promote the therapy based on the first characterization of the first user in relation to the skin-related condition.

14. The method of claim 11 , further comprising:
generating a user microbiome composition feature for the first user based on a first skin-related feature-selection rule of the set of skin-related feature-selection rules; and
generating a user microbiome functional feature for the first user based on a second skin-related feature-selection

Assignees

• Ubiome Inc

Inventors

• Apte Zachary
• Richman Jessica
• Valdivia Catalina
• Almonacid Daniel

Classifications

• G06F19/3418 Primary

  Physics · mapped topic

• G06F19/28

  Physics · mapped topic

• C12Q1/6874

  involving nucleic acid arrays, e.g. sequencing by hybridisation · CPC title

• G16H50/20

  for computer-aided diagnosis, e.g. based on medical expert systems · CPC title

• G06F19/345

  Physics · mapped topic